SBMLLoader tests failing due to java.lang.IllegalArgumentException: URI is not absolute

[matthiaskoenig]

I just tried to do the maven build in eclipse, but some of the tests fail (SBML tests). It looks like a problem in resolving the test files.

- dev branch, commit 87988879d49
- ubuntu 16.04

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 T E S T S
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Running org.insilico.jsbml.core.tests.SBMLLoaderTest
KEY: org.eclipse.e4.core.services.events.IEventBroker
KEY: org.eclipse.e4.core.services.nls.ILocaleChangeService
KEY: org.eclipse.e4.ui.workbench.modeling.EPartService
KEY: org.eclipse.core.runtime.IProgressMonitor
KEY: org.eclipse.fx.core.text.LocaleProvider
KEY: org.eclipse.fx.core.event.EventBus
KEY: org.eclipse.fx.core.di.ScopedObjectFactory
KEY: org.eclipse.fx.core.text.NumberFormatter
KEY: org.eclipse.fx.core.text.DateFormatter
KEY: org.eclipse.fx.core.text.TemporalAccessorFormatter
KEY: org.eclipse.fx.core.observable.SubscriptionRegistry
KEY: org.eclipse.jface.text.IDocumentPartitioner
KEY: org.eclipse.jface.text.source.IAnnotationModel
KEY: org.eclipse.jface.text.IDocument
KEY: org.eclipse.fx.code.editor.Input
KEY: org.eclipse.fx.code.editor.services.ProposalComputer
KEY: org.eclipse.fx.code.editor.services.HoverInformationProvider
KEY: org.eclipse.fx.code.editor.services.SearchProvider
KEY: org.eclipse.fx.code.editor.InputContext
KEY: org.eclipse.fx.code.editor.services.BehaviorContributor
KEY: org.eclipse.fx.code.editor.services.NavigationProvider
KEY: org.eclipse.fx.code.editor.services.EditingContext
KEY: org.eclipse.fx.ui.workbench.renderers.base.services.MaximizationService
KEY: org.eclipse.fx.core.Memento
KEY: org.eclipse.fx.core.command.CommandService
KEY: org.eclipse.fx.core.AppMemento
KEY: org.eclipse.fx.core.text.TranslationService
KEY: org.eclipse.fx.ui.workbench.services.ELifecycleService
KEY: org.eclipse.fx.text.ui.source.SourceViewerConfiguration
KEY: org.eclipse.fx.text.ui.presentation.PresentationReconciler
KEY: org.eclipse.fx.text.ui.source.AnnotationPresenter
KEY: activeOutline
KEY: org.eclipse.fx.code.editor.services.EditorOpener
KEY: org.eclipse.fx.code.editor.fx.e4.EditorContainerService
KEY: org.eclipse.fx.code.editor.fx.services.CompletionProposalPresenter
KEY: org.eclipse.fx.code.editor.fx.services.ContextInformationPresenter
KEY: org.eclipse.fx.code.editor.fx.services.EditorContextMenuProvider
KEY: org.eclipse.fx.text.ui.IUndoManager
KEY: org.eclipse.fx.text.ui.contentassist.IContextInformationValidator
KEY: org.eclipse.fx.ui.di.ResourcePool
KEY: org.eclipse.fx.ui.services.dialog.LightWeightDialogService
KEY: org.eclipse.e4.ui.services.EMenuService
KEY: org.sbml.jsbml.SBMLDocument
Compute...
java.lang.IllegalArgumentException: URI is not absolute
Reading failed
	at java.io.File.<init>(File.java:416)
	at org.insilico.jsbml.core.services.provider.SBMLDocumentLoader.compute(SBMLDocumentLoader.java:73)
	at org.eclipse.e4.core.internal.contexts.ValueComputation.get(ValueComputation.java:62)
	at org.eclipse.e4.core.internal.contexts.EclipseContext.internalGet(EclipseContext.java:262)
	at org.eclipse.e4.core.internal.contexts.EclipseContext.get(EclipseContext.java:228)
	at org.eclipse.e4.core.internal.contexts.EclipseContext.get(EclipseContext.java:599)
	at org.insilico.jsbml.core.tests.SBMLLoaderTest.getSBMLDocumentFromContext_pass(SBMLLoaderTest.java:61)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:50)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:47)
	at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:325)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:78)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:57)
	at org.junit.runners.ParentRunner$3.run(ParentRunner.java:290)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:71)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:288)
	at org.junit.runners.ParentRunner.access$000(ParentRunner.java:58)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:268)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:363)
	at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:264)
	at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:153)
	at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:124)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray2(ReflectionUtils.java:208)
	at org.apache.maven.surefire.booter.ProviderFactory$ProviderProxy.invoke(ProviderFactory.java:156)
	at org.apache.maven.surefire.booter.ProviderFactory.invokeProvider(ProviderFactory.java:82)
	at org.eclipse.tycho.surefire.osgibooter.OsgiSurefireBooter.run(OsgiSurefireBooter.java:95)
	at org.eclipse.tycho.surefire.osgibooter.HeadlessTestApplication.run(HeadlessTestApplication.java:21)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.eclipse.equinox.internal.app.EclipseAppContainer.callMethodWithException(EclipseAppContainer.java:587)
	at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:198)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:134)
	at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:104)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:388)
	at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:243)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:653)
	at org.eclipse.equinox.launcher.Main.basicRun(Main.java:590)
	at org.eclipse.equinox.launcher.Main.run(Main.java:1499)
	at org.eclipse.equinox.launcher.Main.main(Main.java:1472)
Compute...
No doc selected
Compute...
Not a sbml file
Tests run: 4, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 0.065 sec <<< FAILURE! - in org.insilico.jsbml.core.tests.SBMLLoaderTest
serviceActive_pass(org.insilico.jsbml.core.tests.SBMLLoaderTest)  Time elapsed: 0.002 sec
getSBMLDocumentFromContext_pass(org.insilico.jsbml.core.tests.SBMLLoaderTest)  Time elapsed: 0.044 sec  <<< FAILURE!
java.lang.AssertionError: null
	at org.junit.Assert.fail(Assert.java:86)
	at org.junit.Assert.assertTrue(Assert.java:41)
	at org.junit.Assert.assertNotNull(Assert.java:712)
	at org.junit.Assert.assertNotNull(Assert.java:722)
	at org.insilico.jsbml.core.tests.SBMLLoaderTest.getSBMLDocumentFromContext_pass(SBMLLoaderTest.java:63)

getSBMLDocumentFromContext_noDocumentSet(org.insilico.jsbml.core.tests.SBMLLoaderTest)  Time elapsed: 0.001 sec
getSBMLDocumentFromContext_noSBMLFile(org.insilico.jsbml.core.tests.SBMLLoaderTest)  Time elapsed: 0.001 sec

Results :

Failed tests: 
  SBMLLoaderTest.getSBMLDocumentFromContext_pass:63 null

Tests run: 4, Failures: 1, Errors: 0, Skipped: 0